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- Publisher Website: 10.1016/j.ympev.2023.107822
- Scopus: eid_2-s2.0-85162200968
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Article: Museomics and phylogenomics of lovebirds (Psittaciformes, Psittaculidae, Agapornis) using low-coverage whole-genome sequencing
Title | Museomics and phylogenomics of lovebirds (Psittaciformes, Psittaculidae, Agapornis) using low-coverage whole-genome sequencing |
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Authors | |
Keywords | African parrots High-throughput sequencing Historical DNA Museomics Museum genomics Whole-genome re-sequencing |
Issue Date | 21-May-2023 |
Publisher | Elsevier |
Citation | Molecular Phylogenetics and Evolution, 2023, v. 185 How to Cite? |
Abstract | Natural history collections contain specimens that provide important insights into studies of ecology and evolution. With the advancement of high-throughput sequencing, historical DNA (hDNA) from museum specimens has become a valuable source of genomic data to study the evolutionary history of organisms. Low-coverage whole genome sequencing (WGS) has been increasingly applied to museum specimens for analyzing organelle genomes, but is still uncommon for genotyping the nuclear DNA fraction. In this study, we applied low-coverage WGS to phylogenomic analyses of parrots in the genus Agapornis by including both modern samples and historical specimens of ∼100-year-old. Agapornis are small-sized African and Malagasy parrots with diverse characters. Earlier phylogenetic studies failed to resolve the positions of some key lineages, prohibiting a robust interpretation of the biogeography and evolution of these African parrots. Here, we demonstrated the use of low-coverage WGS for generating both mitochondrial and nuclear genomic data, and evaluated data quality differences between modern and historical samples. Our resolved Agapornis phylogeny indicates the ancestor of Agapornis likely colonized Madagascar from Australasia by trans-oceanic dispersal events before dispersing to the African continent. Genome-wide SNPs also allowed us to identify the parental origins of hybrid Agapornis individuals. This study demonstrates the potential of applying low-coverage WGS to phylogenomics and population genomics analyses and illustrates how including historical museum specimens can address outstanding questions regarding the evolutionary history of contemporary lineages. |
Persistent Identifier | http://hdl.handle.net/10722/338773 |
ISSN | 2023 Impact Factor: 3.6 2023 SCImago Journal Rankings: 1.206 |
ISI Accession Number ID |
DC Field | Value | Language |
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dc.contributor.author | Huynh, Stella | - |
dc.contributor.author | Cloutier, Alison | - |
dc.contributor.author | Sin, Simon Yung Wa | - |
dc.date.accessioned | 2024-03-11T10:31:25Z | - |
dc.date.available | 2024-03-11T10:31:25Z | - |
dc.date.issued | 2023-05-21 | - |
dc.identifier.citation | Molecular Phylogenetics and Evolution, 2023, v. 185 | - |
dc.identifier.issn | 1055-7903 | - |
dc.identifier.uri | http://hdl.handle.net/10722/338773 | - |
dc.description.abstract | <p> <span>Natural history collections contain specimens that provide important insights into studies of ecology and evolution. With the advancement of high-throughput sequencing, historical DNA (hDNA) from museum specimens has become a valuable source of genomic data to study the evolutionary history of organisms. Low-coverage whole genome sequencing (WGS) has been increasingly applied to museum specimens for analyzing organelle genomes, but is still uncommon for genotyping the nuclear DNA fraction. In this study, we applied low-coverage WGS to phylogenomic analyses of parrots in the genus Agapornis by including both modern samples and historical specimens of ∼100-year-old. Agapornis are small-sized African and Malagasy parrots with diverse characters. Earlier phylogenetic studies failed to resolve the positions of some key lineages, prohibiting a robust interpretation of the biogeography and evolution of these African parrots. Here, we demonstrated the use of low-coverage WGS for generating both mitochondrial and nuclear genomic data, and evaluated data quality differences between modern and historical samples. Our resolved Agapornis phylogeny indicates the ancestor of Agapornis likely colonized Madagascar from Australasia by trans-oceanic dispersal events before dispersing to the African continent. Genome-wide SNPs also allowed us to identify the parental origins of hybrid Agapornis individuals. This study demonstrates the potential of applying low-coverage WGS to phylogenomics and population genomics analyses and illustrates how including historical museum specimens can address outstanding questions regarding the evolutionary history of contemporary lineages.</span> <br></p> | - |
dc.language | eng | - |
dc.publisher | Elsevier | - |
dc.relation.ispartof | Molecular Phylogenetics and Evolution | - |
dc.rights | This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License. | - |
dc.subject | African parrots | - |
dc.subject | High-throughput sequencing | - |
dc.subject | Historical DNA | - |
dc.subject | Museomics | - |
dc.subject | Museum genomics | - |
dc.subject | Whole-genome re-sequencing | - |
dc.title | Museomics and phylogenomics of lovebirds (Psittaciformes, Psittaculidae, Agapornis) using low-coverage whole-genome sequencing | - |
dc.type | Article | - |
dc.identifier.doi | 10.1016/j.ympev.2023.107822 | - |
dc.identifier.scopus | eid_2-s2.0-85162200968 | - |
dc.identifier.volume | 185 | - |
dc.identifier.eissn | 1095-9513 | - |
dc.identifier.isi | WOS:001054847000001 | - |
dc.identifier.issnl | 1055-7903 | - |